This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. HIV-1 protease and HCV NS3 protease are both enzymes that are required for HIV and HCV infection respectably. Therefore these enzymes are considered ideal targets for anti-viral drugs for the treatment of these diseases. For HIV there are currently 9 protease inhibitors available and several HCV NS3 protease inhibitors are currently in clinical trials. Unfortunately drug-resistance to most of these inhibitors has been observed in replicon studies and/or treated patent populations. Our lab views drug-resistance as a change in molecular recognition such that the target enzyme retains the ability to cleave viral substrates but is no longer able to bind inhibitor. In many HIV-1 protease variants multiple site mutations co-evolve to both decrease the affinity of a particular inhibitor and increase the viability and fitness of the enzyme. Crystallographic studies of HIV-1 protease and HCV NS3 protease in complex with substrates and inhibitors will prove to be valuable in order to determine molecular interactions that mediate substrate recognition while decreasing affinity to a particular inhibitor. Structural insights gained by analyzing high resolution crystal structures of HIV-1 protease and HCV NS3 protease in complex with substrates and inhibitors will serve as a guide to develop high affinity inhibitors that are more robust against emerging drug resistant in both viral systems.